Exhaust popping is unburnt fuel passing through the cylinder(s)...then explodes in the exhaust.
From my point of view,I would first listen to each exhaust pipe to tell if it's more prevelent to one side.
The next step is to remove the spark plugs on that side(or all if necessary).
Inspect each plug and keep track of which one came out of what hole it came from.
A good running cylinder will have a clean plug with a light tan coloring on the enamel tip.
If you see a single plug with soot/black/wet with fuel, you've located the offending cylinder.
A spark quality test and compression would be in order.
Now should all 3 on one side be bad looking,the problem may be in a vacuum line problem or trouble in the carb that feeds that side.
Keep in mind that the bike needs a good charging system to keep it firing well.A near dead battery and no charging system/jumped off to start will not run well at all.